Man page - gmx-dielectric(1)
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apt-get install gromacs-data
Manual
GMX-DIELECTRIC
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
NAME
gmx-dielectric - Calculate frequency dependent dielectric constants
SYNOPSIS
gmx dielectric
[
-f
[<.xvg>]
] [
-d
[<.xvg>]
] [
-o
[<.xvg>]
]
[
-c
[<.xvg>]
]
[
-b
<time>
] [
-e
<time>
] [
-dt
<time>
]
[
-[no]w
]
[
-xvg
<enum>
] [
-[no]x1
]
[
-eint
<real>
] [
-bfit
<real>
]
[
-efit
<real>
] [
-tail
<real>
] [
-A
<real>
]
[
-tau1
<real>
]
[
-tau2
<real>
] [
-eps0
<real>
] [
-epsRF
<real>
]
[
-fix
<int>
] [
-ffn
<enum>
] [
-nsmooth
<int>
]
DESCRIPTION
gmx dielectric calculates frequency dependent dielectric constants from the autocorrelation function of the total dipole moment in your simulation. This ACF can be generated by gmx dipoles . The functional forms of the available functions are:
|
• |
One parameter: y = exp(-a_1 x), |
|||
|
• |
Two parameters: y = a_2 exp(-a_1 x), |
|||
|
• |
Three parameters: y = a_2 exp(-a_1 x) + (1 - a_2) exp(-a_3 x). |
Start values for the fit procedure can be given on the command line. It is also possible to fix parameters at their start value, use -fix with the number of the parameter you want to fix.
Three output files are generated, the first contains the ACF, an exponential fit to it with 1, 2 or 3 parameters, and the numerical derivative of the combination data/fit. The second file contains the real and imaginary parts of the frequency-dependent dielectric constant, the last gives a plot known as the Cole-Cole plot, in which the imaginary component is plotted as a function of the real component. For a pure exponential relaxation (Debye relaxation) the latter plot should be one half of a circle.
OPTIONS
Options to
specify input files:
-f [<.xvg>] (dipcorr.xvg)
xvgr/xmgr file
Options to
specify output files:
-d [<.xvg>] (deriv.xvg)
xvgr/xmgr file
-o [<.xvg>] (epsw.xvg)
xvgr/xmgr file
-c [<.xvg>] (cole.xvg)
xvgr/xmgr file
Other options:
-b <time> (0)
Time of first frame to read from trajectory (default unit ps)
-e <time> (0)
Time of last frame to read from trajectory (default unit ps)
-dt <time> (0)
Only use frame when t MOD dt = first time (default unit ps)
-[no]w (no)
View output .xvg , .xpm , .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[no]x1 (yes)
use first column as x -axis rather than first data set
-eint <real> (5)
Time to end the integration of the data and start to use the fit
-bfit <real> (5)
Begin time of fit
-efit <real> (500)
End time of fit
-tail <real> (500)
Length of function including data and tail from fit
-A <real> (0.5)
Start value for fit parameter A
-tau1 <real> (10)
Start value for fit parameter tau1
-tau2 <real> (1)
Start value for fit parameter tau2
-eps0 <real> (80)
epsilon0 of your liquid
-epsRF <real> (78.5)
epsilon of the reaction field used in your simulation. A value of 0 means infinity.
-fix <int> (0)
Fix parameters at their start values, A (2), tau1 (1), or tau2 (4)
-ffn <enum> (none)
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
-nsmooth <int> (3)
Number of points for smoothing
SEE ALSO
gmx(1)
More information about GROMACS is available at <- http://www.gromacs.org/ >.
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2025, GROMACS development team